|
| Status |
Public on Jun 07, 2024 |
| Title |
Oregon-R_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
wing disc
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: wing disc
Sex: female
developmental stage: 3rd instar wandering
genotype: Oregon-R
cut&run antibody: anti-H4K20me1 (ThermoFisher MA5-18067)
|
| Growth protocol |
Animals were raised at 25C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
20 wing imaginal discs were individually dissected in 1xPBS from 3rd instar wandering larvae. Following CUT&RUN protocol, DNA fragments in the supernatant (diffused out of the nucleus) were prepared and sequenced
DNA libraries were prepared using ThruPLEX DNA-seq Kit (Takara) and DNA Unique Duel Index Kit
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| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
H4K20me1.vs.no_primary.peaks.bed
OregonR_spikeNorm_K20me1_allReps_avg.bw
|
| Data processing |
Adapters were trimmed using bbduk
Reads were aligned to dm6 with bowtie2 and converted to bam format
Reads with quality score < 5 were removed via samtools and duplicates were removed
Bam files were converted to bed format with bedtools
bed files were scaled by values generated using yeast DNA spike-ins by Spike-in normalized Reads Per Million mapped reads in the negative Control (SRPMC) with bedtools genomeCoverage then converted to BigWig coverage files with ucsctools wigToBigWig
Peaks were called using the csaw package and edgeR. Aligned reads were binned into 150bp windows with a 50bp slide. Bins with a log(2) > 2 above background were retained. Windows were normalized for compositional bias and windows in enriched in Oregon-R_K20me1 relative to Oregon-R_no_primary were calculated using edgeR. Windows within 1kb were merged and windows with log(2)FC > 1 and FDR < 0.05 were called peaks
Assembly: dm6
Supplementary files format and content: H4K20me1.vs.no_primary.peaks.bed bed file containing genomic coordinates of enriched regions in Oregon-R_K20me1 relative to Oregon-R_no_primary (l2fc > 1) using the csaw package and edgeR
Supplementary files format and content: OregonR_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: OregonR_spikeNorm_no_primary_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R_no_primary. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: HWT_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in HWT. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: K20A_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in H4K20A. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: K20R_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: HWT_His4rnull_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in HWT, His4rnull. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: K20R_His4rnull_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R, His4rnull. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: Set8null_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in Set8null. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: Set8wt_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in Set8wt. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: Set8rg_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in Set8rg. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: OregonR_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R replicate 1
Supplementary files format and content: OregonR_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R replicate 2
Supplementary files format and content: OregonR_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R replicate 3
Supplementary files format and content: OregonR_spikeNorm_no_primary_rep1.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R_no_primary replicate 1
Supplementary files format and content: OregonR_spikeNorm_no_primary_rep2.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R_no_primary replicate 2
Supplementary files format and content: OregonR_spikeNorm_no_primary_rep3.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R_no_primary replicate 3
Supplementary files format and content: HWT_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in HWT replicate 1
Supplementary files format and content: HWT_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in HWT replicate 2
Supplementary files format and content: K20A_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in H4K20A replicate 1
Supplementary files format and content: K20A_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in H4K20A replicate 2
Supplementary files format and content: K20R_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R replicate 1
Supplementary files format and content: K20R_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R replicate 2
Supplementary files format and content: K20R_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R replicate 3
Supplementary files format and content: HWT_His4rnull_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in HWT, His4rnull replicate 1
Supplementary files format and content: HWT_His4rnull_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in HWT, His4rnull replicate 2
Supplementary files format and content: HWT_His4rnull_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in HWT, His4rnull replicate 3
Supplementary files format and content: K20R_His4rnull_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R, His4rnull replicate 1
Supplementary files format and content: K20R_His4rnull_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R, His4rnull replicate 2
Supplementary files format and content: Set8null_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in Set8null replicate 1
Supplementary files format and content: Set8null_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in Set8null replicate 2
Supplementary files format and content: Set8null_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in Set8null replicate 3
Supplementary files format and content: Set8wt_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in Set8wt replicate 1
Supplementary files format and content: Set8wt_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in Set8wt replicate 2
Supplementary files format and content: Set8wt_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in Set8wt replicate 3
Supplementary files format and content: Set8rg_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in Set8rg replicate 1
Supplementary files format and content: Set8rg_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in Set8rg replicate 2
Supplementary files format and content: Set8rg_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in Set8rg replicate 3
Library strategy: CUT&RUN
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| |
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| Submission date |
May 31, 2024 |
| Last update date |
Jun 07, 2024 |
| Contact name |
Robert J. Duronio |
| E-mail(s) |
duronio@med.unc.edu
|
| Organization name |
UNC Chapel Hill
|
| Street address |
250 Bell Tower Dr., Gen. Sci. Bldg. 3356, CB7100
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL30203 |
| Series (1) |
| GSE268819 |
Drosophila melanogaster Set8 and L(3)mbt function in gene expression independently of histone H4 lysine 20 methylation [H4K20me1_CUT&RUN] |
|
| Relations |
| BioSample |
SAMN41624093 |
| SRA |
SRX24767813 |
